Super-enhancer lncRNA Array Service

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Arraystar Super-enhancer lncRNA Arrays are designed to systematically profile lncRNAs transcribed from super-enhancer (SE) regions along with corresponding SE-regulated protein coding genes. We offer the complete Super-enhancer LncRNA array service, from sample to publishable data!

Benefits

• Comprehensive collection of SE-lncRNAs and super-lncRNAs >>
• Simultaneous profiling of the target mRNA genes associated with SE-lncRNAs >>
• Entire sets of transcription factors and oncogenes >>
• Detailed annotations for SE-lncRNA, super-enhancer, and targets >>
• Unambiguous and reliable SE-lncRNA isoform detection >>
• Efficient target labeling for sensitive detection of labile SE-lncRNAs >>
• Superior quantification of LncRNAs over RNA-seq >>

 

Service NameCatalog NoDescriptionFormatPrice
Arraystar Human SE-lncRNA Array AS-S-SE-H 7753 SE-lncRNAs and 7040 mRNAs 8*15K
Arraystar Mouse SE-lncRNA Array AS-S-SE-M 8222 SE-lncRNAs and 6385 mRNAs 8*15K

Powerful SE-lncRNA collection
• LncRNA foundation using Arraystar premium transcriptome and lncRNA databases for comprehensive, high quality systematic lncRNA compilation.
  - Reliable lncRNAs comprehensively sourced from public databases, such as Refseq, UCSC knownGene, GENCODE, lncRNAdb, RNAdb, NRED and lncRNA Catalogs.
  - Gold standard lncRNAs for well annotated, experimentally studied and Pubmed indexed lncRNAs.
  - Manual curation of lncRNAs from continuous scientific publication review and selection.
• Super-enhancer regions are cataloged in the dbSUPER database.
• SE-lncRNAs are identified by mapping the lncRNAs to the super-enhancer regions.

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Simultaneous profiling of SE-lncRNAs and their target genes on the same array, to experimentally observe, quantify, correlate and establish accurate regulatory relationships.

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SE-lncRNAs transcript isoforms are unambiguously, specifically and reliably detected by unique exon or splice-junction array probes (Fig. 1), with high sensitivity at one transcript per cell.
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Figure 1. The unique sequence of Probe #2’ specifically detects lncRNA CCAT1-L isoform.

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Detailed annotation for super-enhancers, SE-lncRNAs and their associated target coding genes.

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SE-lncRNA_annotatoinFigure 2. Comprehensive annotations of SE-lncRNAs and their target coding genes.
Annotations of SE-lncRNA include: transcript ID; gene symbol and alias; genomic locus, sequence and length; subcellular localization; associated cell or tissue types, cancers and disease; overlapped superenhancer information
Annotations of target coding genes include: overlapped gene symbol and ID; proximal gene symbol and gene ID.

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Arraystar has developed the first commercially available SE-lncRNA Arrays for human, mouse, and rat to comprehensively, systematically and sensitively profile the SE-lncRNAs and their cis- or trans-regulated coding genes on the same array. 

What are super enhancer lncRNAs?

Super-enhancer lncRNA (SE-lncRNAs), emerging as a novel class of master RNA regulators, is a special set of long noncoding RNAs transcribed from super-enhancer genomic loci. SE-lncRNAs, together with super-enhancers, activate the nearby gene expression by mechanisms of transcription factor trapping, chromatin looping, chromatin modification, PolII loading, and release of transcriptional repressor (Fig. 1). Also, SE-lncRNAs are increasingly found to trans-activate target genes [1]. SE-lncRNA have been associated with many human diseases and their expression manifests in profound phenotypic changes [1-3]

 

SE-LncRNA-BG
Fig. 1. SE-lncRNAs activate the target gene promoter by multiple mechanisms

Master regulator RNAs in biology and disease

Super-enhancer lncRNAs play master regulatory roles in diverse gene expression programs that ultimately determine the cell types, cell identities, and diseases. For example, SE-lncRNAsCERNA and DRRRNA auto-regulate the master transcription factor MyoD and myogenic genes to turn on myogenesis [2]. Many SE-lncRNAs are intimately involved in cancers. A good example can be CCAT1-L, upstream of MYC gene. It mediates enhancer-promoter loop formation, activates MYC expression and promotes colorectal cancer progression [3].

The super-enhancer lncRNAs, emerged from hidden just recently, are now a scientific gold mine in the research of any fields of biology and disease. Arraystar has developed the SE-lncRNA profiling solution to simultaneously profile SE-lncRNAs, target genes, transcription factors and oncogenes, to accelerate the investigation of SE lncRNAs and the coding genes under their control. 

References
1. Bradner JE, Hnisz D, Young RA: Transcriptional Addiction in Cancer. Cell 2017, 168(4):629-643.[PMID: 28187285]
2. Alvarez-Dominguez JR, Knoll M, Gromatzky AA, Lodish HF: The Super-Enhancer-Derived alncRNA-EC7/Bloodlinc Potentiates Red Blood Cell Development in trans. Cell Rep 2017, 19(12):2503-2514.[PMID: 28636939]
3. Xiang JF et al: Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res 2014, 24(5):513-531.[PMID: 24662484]
 

Human SE-lncRNA Array specifications

Total Number of Distinct Probe 14873
Probe Length 60 nt
Probe Selection Region Probes targeting SE-lncRNA transcript-specific splice junctions or exons
Probe specificity Transcript-specific
Labeling Method An efficient and robust linear amplification method to produce fluorescently labeled target cRNA for sensitive detection of transcripts at even low copy numbers.
SE-lncRNAs & Super-lncRNAs 7753
SE-lncRNA targeted coding genes 7040
SE-lncRNAs sources • Gold standard lncRNAs and reliable lncRNAs from Arraystar Premium transcriptome databases are mapped to the super-enhancer loci catalogued in the dbSUPER database. The lncRNAs overlapped with the super-enhancers are identified and annotated as SE-lncRNAs.
• Enhancer-lncRNAs from literature [4, 5], whose genomic loci overlap with the cataloged super-enhancer loci.
Super-lncRNAs sources Super-lncRNAs are long noncoding RNAs which form RNA:DNA:DNA triplex with multiple anchor DNA sites within the super-enhancers and recruit regulators to the super-enhancers. Super-lncRNAs influence chromatin organization and act as spatial amplifiers for key tissue-specific genes associated with super-enhancers[6].
SE-lncRNA targeted coding genes sources The Refseq genes that either overlap with the SE-lncRNA genomic loci or whose transcription start sites (TSS) fall within 50 kb of the SE-lncRNA genomic loci boundaries are collected as SE-lncRNA targeted coding genes. These genes include 3153 transcription factors (TFs) from TF checkpoint database and 1448 cancer genes from Bushman Lab database.
Array Format 8 * 15K


Mouse SE-lncRNA Array specifications

Total Number of Distinct Probe 14637
Probe Length 60 nt
Probe Selection Region Probes targeting SE-lncRNA transcript-specific splice junctions or exons
Probe specificity Transcript-specific
Labeling Method An efficient and robust linear amplification method to produce fluorescently labeled target cRNA for sensitive detection of transcripts at even low copy numbers.
SE-lncRNAs 8222
SE-lncRNA targeted coding genes 6385
SE-lncRNAs sources Gold standard lncRNAs and reliable lncRNAs from Arraystar Premium transcriptome databases are mapped to the super-enhancer loci catalogued in the dbSUPER database. The lncRNAs overlapped with the super-enhancers are identified and annotated as SE-lncRNAs.
SE-lncRNA targeted coding genes sources The Refseq genes that either overlap with the SE-lncRNA genomic loci or whose transcription start sites (TSS) fall within 50 kb of the SE-lncRNA genomic loci boundaries are collected as SE-lncRNA targeted coding genes. These genes include 2883 transcription factors (TFs) from TF checkpoint database and 593 cancer genes from SBCDDB database.
Array Format 8 * 15K

 

 

Arraystar's specially-designed SE-LncRNA Arrays are available only through our SE-LncRNA Array service. We provide full-service SE-LncRNA Array profiling, from sample preparation to in-depth data analysis. Our step-by-step quality controls are designed to ensure you get the most reliable results. Just send us your samples, and we'll do the rest!

Please refer to Sample Submission for details in how to get your project started.
•  RNA isolation (Optional)
•  RNA QC
•  cDNA synthesis
•  Target preparation by efficient labeling with Cy3
•  Array hybridization, washing, and scanning
•  Data extraction, analysis and summarization